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UPDATE 2/28/12: Hasbro has responded to the edit with the following statement from their public relations representative Nicole Angello:
"The 'My Little Pony Friendship is Magic' series has always been about acceptance and inclusion, and the series strives to convey that through the playful antics of a diverse cast of characters. Some viewers felt that aspects of the episode 'The Last Roundup' did not stay true to the core message of friendship which is the heart and soul of the series. Hasbro Studios decided to make slight audio alterations to this single episode."
It should be noted that, as I've personally confirmed with my own purchase, the episode remains unedited on the Friendship Express DVD. Whether that will change with subsequent production runs or later discs/box sets remains uncertain, but Hasbro's statement seems to imply this is going to remain a series-wide alteration, not just an iTunes edit as some have speculated.
Quick clip showing the edit that is Derpy's new voice after the episode "The Last Roundup" was re-uploaded to iTunes earlier today. Video quality's not the best and I was a bit hasty getting this up, but it drives the point home.